Showing : featureCounts • reset
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Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 22 days ago by ★ 3.5k • written 5 weeks ago by • 0
0
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0
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119
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
7 weeks ago barrypraveen • 0
2
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9
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499
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featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
12 weeks ago • updated 11 weeks ago Hilary ▴ 30
0
votes
2
replies
317
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 3 months ago by ★ 3.5k • written 6 months ago by • 0
0
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0
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106
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Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
3 months ago yao hua • 0
0
votes
1
reply
269
views
Subread installation on Linux ARM64
subread featureCounts
updated 3 months ago by ▴ 350 • written 4 months ago by • 0
0
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1
reply
150
views
DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2 featurecounts
updated 4 months ago by ★ 1.2k • written 4 months ago by • 0
3
votes
3
replies
680
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 4 months ago by 47k • written 4 months ago by • 0
0
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1
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550
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FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 5 months ago by ★ 1.2k • written 5 months ago by • 0
1
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1
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629
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Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 6 months ago by 47k • written 6 months ago by • 0
0
votes
0
replies
189
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 6 months ago by ★ 2.9k • written 6 months ago by • 0
2
votes
3
replies
358
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 6 months ago by 47k • written 6 months ago by • 0
2
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2
replies
316
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
7 months ago dario.beraldi • 0
0
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0
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187
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
7 months ago rridley3 • 0
0
votes
2
replies
690
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
8 months ago KMS ▴ 10
0
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1
reply
1.3k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 10 months ago by 47k • written 10 months ago by • 0
0
votes
1
reply
418
views
fetaure counts err
featurecounts
updated 10 months ago by ★ 3.5k • written 10 months ago by • 0
0
votes
1
reply
414
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
12 months ago NIK • 0
1
vote
1
reply
781
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 12 months ago by 47k • written 12 months ago by • 0
2
votes
1
reply
844
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 12 months ago by ★ 1.2k • written 12 months ago by • 0
0
votes
4
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985
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featureCounts: 0% successfully assigned fragments
featureCounts
12 months ago KMS ▴ 10
1
vote
4
replies
693
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
13 months ago Chise ▴ 10
3
votes
11
replies
2.0k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
13 months ago Sarah_piggy ▴ 10
1
vote
4
replies
847
views
Subread installation
subread featureCounts
13 months ago Lucy ▴ 60
1
vote
5
replies
1.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
15 months ago Lucy ▴ 60
2
votes
2
replies
3.3k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
17 months ago Chise ▴ 10
4
votes
4
replies
2.9k
views
FeatureCounts
counts subread RNASeq featurecounts
18 months ago k___ ▴ 20
0
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2
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900
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 7 months ago by • 0 • written 21 months ago by • 0
1
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1
reply
642
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 22 months ago by ★ 3.5k • written 22 months ago by • 0
1
vote
3
replies
2.7k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 23 months ago by ★ 3.5k • written 23 months ago by ▴ 10
4
votes
5
replies
1.3k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
24 months ago • updated 22 months ago Konstantinos Yeles ▴ 80
2
votes
2
replies
1.2k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 2.2 years ago by ▴ 350 • written 2.2 years ago by • 0
6
votes
26
replies
4.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.5 years ago by ▴ 350 • written 8.2 years ago by 7.8k
0
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0
replies
457
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
2.6 years ago martinag.work • 0
0
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1
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2.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
updated 2.9 years ago by ★ 1.2k • written 2.9 years ago by ▴ 80
1
vote
2
replies
2.5k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
3.2 years ago chatterjee.arumoy ▴ 10
2
votes
3
replies
1.4k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 3.5 years ago by 63k • written 3.5 years ago by • 0
4
votes
2
replies
797
views
bwa mem to feature Counts
bwa mem featureCounts
updated 3.7 years ago by ★ 1.2k • written 3.7 years ago by • 0
0
votes
2
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657
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 3.8 years ago by ★ 3.5k • written 3.8 years ago by • 0
4
votes
3
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3.5k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 3.9 years ago by ★ 3.5k • written 3.9 years ago by ▴ 80
1
vote
2
replies
1.7k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 3.9 years ago by 47k • written 3.9 years ago by • 0
1
vote
1
reply
606
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 4.0 years ago by 47k • written 4.0 years ago by ▴ 40
5
votes
11
replies
2.8k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 13 months ago by ▴ 10 • written 4.1 years ago by ▴ 120
3
votes
7
replies
1.4k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 4.1 years ago by 47k • written 4.1 years ago by • 0
1
vote
1
reply
2.1k
views
featureCounts for ATAC-seq
subread featurecounts atac
updated 4.1 years ago by ★ 3.5k • written 4.1 years ago by ▴ 10
7
votes
5
replies
2.8k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 4.1 years ago by 47k • written 4.1 years ago by ▴ 60
2
votes
6
replies
1.3k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 4.2 years ago by ★ 3.5k • written 4.2 years ago by • 0
1
vote
2
replies
967
views
Problem with importing text file in featureCounts
Rsubread featureCounts
updated 4.2 years ago by 47k • written 4.2 years ago by • 0
3
votes
2
replies
1.6k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq featureCounts STAR minMQS mapping quality score
updated 4.3 years ago by 47k • written 4.3 years ago by ▴ 20
0
votes
5
replies
1.5k
views
featureCounts error : SAM_pairer_iterate_tags
subread featureCounts
updated 4.3 years ago by 47k • written 4.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
Sure, noted.
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would do the job.
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by ansleyharralson • 0
Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.
Votes
WGCNA coupled with differential expression analysis: question about baseline module detection
WGCNA with paired samples
Comment: Question on constructing design matrix and defining contrasts for analysis
Comment: Question on constructing design matrix and defining contrasts for analysis
Answer: Question on constructing design matrix and defining contrasts for analysis
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